[BioSQL-l] installation.....IO/String problem

[mrphysh at juno.com]

I am having trouble with database retrieval from online databases. 
This is an install problem.(?)..I am running Linux (Ubuntu).........
I did these, following the documentation.  from cpan>
install Bundle::CPAN

install Module::Build  #one of the many help files said to do this
install Bundle;;BioPerl
force install B/BI/BIRNEY/bioperl-1.4.tar.gz

The ftp found the file and went to work.  After many minutes, at the end, this what I saw:

t/Variation _IO.............................FAILED tests 15,20,25
          Failed 3/25  88% okay
t/WABA...............................ok
t/XEMBL_DB...........................ok
t/XEMBL_DB...........................SOAP::lite and/or XML::DOM not installed.  this means that Bio::DB::XEMBL module is not usable. Skipping test
t/XEMBL_DB...........................ok
failed test                      stat               wstat   total     fail     failed   list of failed
t/BioFetch_DB.t							27	4	14%	8 20 21 27


t/DB.t								78	2	2.5%	30 31


t/EMBL_DB.t							15	3	20$	6 13 14

t/Ontology.t				9	2304		50	100	200%	1-50

t/TreeIO.t							41	1	2.4%	42

t/Variation_IO.t						25	3	12%	15 20 25

t/simpleGPparser.t			9	2304		98	196	200%	1-98

18 SUBTESTS SKIPPED
fAILED 7/179 TEST SCRIPTS 96.09%  159/8268 SUBTEST FAILED 98% OKAY
MAKE:  ****[TEST DYNAMIC] ERROR 225
/USR/BIN/MAKE_TEST   --  not ok
Running make install

Warning:  you do not have permission to install into /usr/local/lib/perl/5.8.8 at /usr/share/perl/5.8/ExUtils
/install.pm line 114

can't open file /usr/local/lib/perl/5.8.8/auto/Bio/.packlist:  permission denied at /usr/share/perl/5.8/ExtUtils?Install.pm line 209
writing /usr/local/lib/perl/5.8.8/auto/Bio/.packlist
make:  ***  [pure_site_install  error13
   /usr/bin/make_install   --- NOT OKAY
        you may have to u to root to install the package

cpan>               #this is all my typing

 I have this little script (from a tutorial) and others that are similar

use Bio::Perl;
# this script will only work with an internet connection
# on the computer it is run on
$seq_object = get_sequence('swissprot',"ROA1_HUMAN");
write_sequence(">roa1.fasta",'fasta',$seq_object);

I quit CPAN and type

~~  perl ee_use_bioperl.pl

######I get

you system does not have of LWP, HTTP::Request::Common, IO::String installed so the DB retrieval method is not available.  
Full Error message is:

 at /usr/local/hsare/ perl/5.8.8/bio/perl.pm line 464
           Bio::perl::Get_sequence('swissprot','ROA!_HUMAN') called at ee_use_bioperl.pl line 4
john at john-desktop:~/bbs$

#############

I feel that I am making progress but need assistance on this roadblock.  My ideas and questions.

Is this a perl issue.  I am using the perl 5.8.8 that came with the Ubuntu
I am much aware of the permissions aspect of Linux.  The documentation says little about this.  Is this where I am hanging up?
  (As you all know, Ubuntu has no logon as root but uses a sudu permissions system)
I have reloaded the bioperl many many itmes.  I do not want to sound 'windowie' but should I uninstall, then install?
The errors always point to IO::string.  I can find String.pm files in the /usr/hsare/perl5/debconf/Element  but nowhere else.
I cannot find a /IO/  (an IO folder) anywhere.

please and thanks
John Brigham 


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